SMTL ID : 8buf.3 (2 other biounits)

Structure of DDB1 bound to Z12-engaged CDK12-cyclin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

17 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: K.172, I.224, H.265, N.266, R.267, Y.275 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: K.564, Y.591, L.599, R.600, T.601 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: N.650, H.691, L.692, Q.693, E.694 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: C.603, N.604, Y.606 Ligand excluded by PLIP SO4.5: 8 residues within 4Å: Chain A: S.466, S.467, S.468, H.505, R.547, V.549, F.551, T.560 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: R.133, V.199, S.200, L.201, R.202 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: K.423, S.572, Y.613, L.614 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: C.22, V.23, T.24, N.266, T.319 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: A.158, F.159, N.160 Chain B: R.273 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: E.316, L.317, S.318 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.162 Chain B: S.283 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: P.282, S.283, A.284 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain B: R.275 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: M.113, K.153, S.155 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: Y.141, K.144, K.145 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: R.237, P.247, V.248, D.249 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: R.52, Y.53, R.96 Ligand excluded by PLIP

1 x RW6: 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one(Non-covalent)

RW6.10: 22 residues within 4Å: Chain A: N.607, I.609, R.628, R.647, F.649 Chain B: I.25, G.26, E.27, G.28, V.33, K.35, A.46, K.48, V.79, F.105, Y.107, M.108, D.109, H.110, D.111, L.158, A.168 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.609, A:R.628, B:I.25, B:L.158 Hydrogen bonds: A:R.628, B:M.108, B:M.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozicka, Z. et al., Design principles for cyclin K molecular glue degraders. Nat.Chem.Biol. (2024)

Release Date

2023-09-13

Peptides

DNA damage-binding protein 1: A
Cyclin-dependent kinase 12: B
Cyclin-K: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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